Originally published as Genetics Published Articles Ahead of Print on June 8, 2009.

Genetics, Vol. 182, 1303-1311, August 2009, Copyright © 2009
doi:10.1534/genetics.109.102871

Identification of a New Rice Blast Resistance Gene, Pid3, by Genomewide Comparison of Paired Nucleotide-Binding Site–Leucine-Rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes

Junjun Shang^1,*,, Yong Tao^1,*,, Xuewei Chen^1,*,, Yan Zou^*,, Cailin Lei, Jing Wang^*,, Xiaobing Li^*, Xianfeng Zhao^*, Meijun Zhang, Zhike Lu, Jichen Xu^*, Zhukuan Cheng^*, Jianmin Wan and Lihuang Zhu^*,2

^* State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China, Institute of Crop Research, Chinese Academy of Agricultural Sciences, Beijing 100081, China, Graduate School of Chinese Academy of Sciences, Beijing 100101, China and Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China

² Corresponding author: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
E-mail: lhzhu{at}genetics.ac.cn

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of the major class of resistant gene family, the nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family, between 93-11 (indica) and Nipponbare (japonica) with a focus on their pseudogene members. We found great differences in either constitution or distribution of pseudogenes between the two genomes. According to this comparison, we designed the PCR-based molecular markers specific to the Nipponbare NBS–LRR pseudogene alleles and used them as cosegregation markers for blast susceptibility in a segregation population from a cross between a rice blast-resistant indica variety and a susceptible japonica variety. Through this approach, we identified a new blast resistance gene, Pid3, in the indica variety, Digu. The allelic Pid3 loci in most of the tested japonica varieties were identified as pseudogenes due to a nonsense mutation at the nucleotide position 2208 starting from the translation initiation site. However, this mutation was not found in any of the tested indica varieties, African cultivated rice varieties, or AA genome-containing wild rice species. These results suggest that the pseudogenization of Pid3 in japonica occurred after the divergence of indica and japonica.

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